Actions undertaken by Governor Eugene Talmadge had caused the state's colleges to lose accreditation. Arnall unseated Talmadge in the 1942 primary, 174,757 (57.7 percent) to 128,394 (42.4 percent).[3] Without Republican opposition, Arnall hence became the youngest governor then serving in the United States.

Arnall obtained the repeal of the poll tax, ratification in 1945 of a new state constitution, and a state employee merit system. He also retired the Georgia state debt. When young men were drafted into the armed forces during World War II, Arnall argued that youths old enough to fight in war should be able to vote for their country's leadership. He succeeded in lowering the voting age to eighteen more than two decades before the 26th Amendment to the United States Constitution implemented that change nationally. Georgia thus became the first state to grant the franchise to 18-year olds. Arnall also removed the prison system under the governor's control. He established a board of corrections to oversee state prisons and a pardon and parole board to handle such requests. He removed the University of Georgia from political machinations,[4] and he led efforts to prevent a governor from exercising dictatorial powers, as opponents of Governor Eugene Talmadge had allegedly stated, had occurred during that administration. Arnall's reforms won him attention from the national press.

Eugene Talmadge was elected governor once again in 1946, but he died a month before he was scheduled to take office in January 1947. The state legislature then elected Talmadge's son, Herman Talmadge, as governor. Arnall refused to resign the office during the controversy, and the younger Talmadge ended up locking Arnall out of his office in the state capitol. Arnall soon endorsed Melvin E. Thompson's unsuccessful claim to the office.

After leaving office, Arnall worked as an attorney and a businessman in Atlanta, founding Arnall Golden & Gregory (now Arnall Golden Gregory LLP), which continues to be one of Atlanta's leading law firms. For a time one of his law partners was later U.S. RepresentativeElliott Levitas. Arnall served in the Truman administration for a short time as Director of the Office of Price Administration. Truman offered Arnall the post of Solicitor General but he declined in order to return to private practice.

Arnall's last campaign was for governor was in 1966. His principal opponent for the nomination was Lester Maddox, an Atlanta businessman who had hoisted ax handles as a symbol of his opposition to desegregation. Maddox shelled Arnall as "the granddaddy of forced racial integration ... a candidate who would never raise his voice or a finger - much less an ax handle - to protect the liberty of Georgia."[5] Arnall practically ignored Maddox and concentrated his fire on Republican Howard Callaway, on whom Arnall had compiled a dossier which he said would guarantee Republican defeat in the general election. Arnall won a plurality of the vote in the primary but was denied the required majority because of support for future U.S. PresidentJimmy Carter, then an obscure state senator from Plains, Georgia. Arnall barely campaigned in the run-off election, and the result was a surprising victory for Maddox. After his own elimination, Carter refused to endorse Arnall, but he did formally support Maddox in the general election against the Callaway.[6]

Maddox defeated Arnall in the runoff, 443,055 to 373,004. The civil rights activist Martin Luther King, Jr., denounced what he called "a corroding cancer in the Georgia body politic. Georgia is a sick state produced by the diseases of a sick nation. This election revealed that Georgia is desperately competing with Mississippi for the bottom."[7]MayorIvan Allen, Jr., of Atlanta, who once worked for Arnall's law firm, blamed Arnall's loss on the "combined forces of ignorance, prejudice, reactionism, and the duplicity of many Republican voters," many of whom are believed to have voted for Maddox in the Democratic runoff on the theory that Maddox would be a weaker opponent for Callaway than would have been Arnall.[7] Stunned Arnall backers announced a write-in candidacy for the general election, a move which impacted Callaway more than it did Maddox. In the general election, Callaway finished in the tabulation with a slight plurality over Maddox. Arnall received more than 52,000 write-in ballots and led the field in one county, Liberty County in the southeastern portion of the state. Under the election rules then in effect, the state legislature was required to select a governor from the two candidates with the highest number of votes. With the legislature overwhelmingly dominated by Democrats and despite court challenges, Maddox became governor early in 1967.[8]